[gmx-users] How to increase the tolerance for conjugate gradient minimization

Erik Lindahl lindahl at cbr.su.se
Sat Jun 19 23:02:50 CEST 2010

Hi Arthur,

Two answers:

It's a pretty fundamental result on numerical analysis that you can only achieve a tolerance that is sqrt(EPS), where EPS is your floating-point accuracy. If you need better tolerance you might have to try double precision.

Be careful to use e.g. switched interactions and a cutoff buffer, and you might want to emply L-BFGS minimization in the endgame.

However: this assumes you really need extremely low tolerance - the only normal application where that is the case is normal modes.



On Jun 4, 2010, at 7:54 PM, Arthur Roberts wrote:

> Hi, all,
> Is there a way to increase the tolerance for Conjugate Gradient energy minimization?
> It seems that I can only get a Tolerance (Fmax) = 1e-4
> emtol doesn't seem to do the trick.  I tried several values.
> Much appreciated,
> Art
> Dr. Arthur Roberts, Ph.D.
> University of California, San Diego
> Skaggs School of Pharmacy and Pharmaceutical Sciences
> 9500 Gilman Drive #0703
> La Jolla, CA 92093-0703
> email: aroberts99163 at yahoo.com
> cell: 206-850-7468
> skype=aroberts92122
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Erik Lindahl <lindahl at cbr.su.se>
Professor, Computational Structural Biology
Center for Biomembrane Research & Swedish e-Science Research Center
Department of Biochemistry & Biophysics, Stockholm University
Tel: +468164675 Cell: +46703844534

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